[gmx-users] memory excess error of Tip4p/Ice model

Dear gromacs users I have performed MD simulation using Tip4p/ice model, which is copied from [http://www.sklogwiki.org/SklogWiki/index.php/GROMACS_topology_file_for_the_TIP4P/Ice_model] The MD actually works and the output structure looks fine. However, after 11ns run, the run was suddenly sto

[gmx-users] Smooth decay of interaction

Dear gmx users I would like to smoothly decrease the strength of the interaction of coulomb & vdw to zero, without Ewald. According to the tutorial, I made .mdp file by myself. MD calculation could run actually, but I am a little anxious.. Could you please tell me the following file looks corre

Re: [gmx-users] Diffusion beyond periodic boundary

9:17:12 >> Subject: Re: [gmx-users] Diffusion beyond periodic boundary >> >> Hi Kenji, >> >> That's not possible. But why would you need that? It's not very hard to >> make the changes required in gmx_trjconv.c >> >> Cheers, >> &

Re: [gmx-users] Diffusion beyond periodic boundary

; Canada >> -- >> gmx-users mailing list gmx-users@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >> * Please don't post (un)subscr

[gmx-users] Diffusion beyond periodic boundary

Dear All I have performed MD run with periodic boundary condition, which system is consist of water and LJ particles. I would like to know the time dependence of the dislocated distance (diffusion) from the starting time (t=0). Firstly, I made pdb file of the trajectory, then calculated the dis

Re: [gmx-users] making .top file of new LJ in Water

>> >> [ molecules ] >> SOL 1088 >> LJN 1 >> >> Swap them like this >> >> Cheers, >> EB >> -Original Message- >> From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] >> On Behalf Of Ken

[gmx-users] making .top file of new LJ in Water

" [ system ] GAS Hydrate [ molecules ] LJN 1 SOL 1088 ======- Kenji Mochizuki -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/S

Re: [gmx-users] How to merge Self-made ammonia .top with tip4p

ul >> To: Discussion list for GROMACS users >> Date: 2012-12-06 22:56:19 >> Subject: Re: [gmx-users] How to merge Self-made ammonia .top with tip4p >> >> >> On 12/6/12 6:09 AM, Kenji Mochizuki wrote: >> > Dear GMX users >> > >> >

[gmx-users] How to merge Self-made ammonia .top with tip4p

Dear GMX users Could you tell me how to make the topology file for ammonia in tip4p water? I made topology file for ammonia by hand, as shown at end. MD dose work when system has only ammonia molecules. For ammonia in water, I had though it needed to add just two line at the top of .top file.